December 2010 - beg-bogas@psb.ugent.be

[Beg-bogas] [BOGAS] #150: sequence to GV
by BOGAS 03 Apr '12

03 Apr '12

#150: sequence to GV ------------------------------+--------------------------------------------- Reporter: liste | Owner: thabe Type: enhancement | Status: new Priority: major | Milestone: BOGAS_v4 Component: ArteminiServices | Version: Keywords: | ------------------------------+--------------------------------------------- need a diff system of getting seq to GV (art??), because loading full chrom of Medtr already is difficult. save will also not work due to server upload file limit -- Ticket URL: <http://psbsvn01/trac/BOGAS/ticket/150> BOGAS <http://bioinformatics.psb.ugent.be/webtools/bogas> Bioinformatics Online Genome Annotation Service

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[Beg-bogas] [BOGAS] #151: also a bogas login link on the genome page
by BOGAS 03 Apr '12

03 Apr '12

#151: also a bogas login link on the genome page -------------------------+-------------------------------------------------- Reporter: thpar | Owner: liste Type: enhancement | Status: new Priority: trivial | Milestone: BOGAS_v4 Component: Website | Version: Keywords: | -------------------------+-------------------------------------------------- http://bioinformatics.psb.ugent.be/genomes/ -- Ticket URL: <http://psbsvn01/trac/BOGAS/ticket/151> BOGAS <http://bioinformatics.psb.ugent.be/webtools/bogas> Bioinformatics Online Genome Annotation Service

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[Beg-bogas] [BOGAS] #161: prot DOM section and figure
by BOGAS 30 Mar '12

30 Mar '12

#161: prot DOM section and figure ---------------------+------------------------------------------------------ Reporter: liste | Owner: liste Type: task | Status: new Priority: major | Milestone: BOGAS_v4 Component: Website | Version: Keywords: | ---------------------+------------------------------------------------------ check section + fig to see if multiple occurrences of the same domain is available. (if map to hash -> no, replace by array or so) -- Ticket URL: <http://psbsvn01/trac/BOGAS/ticket/161> BOGAS <http://bioinformatics.psb.ugent.be/webtools/bogas> Bioinformatics Online Genome Annotation Service

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[Beg-bogas] FW: Ectocarpus siliculosus
by Meijer, Harold 20 Dec '10

20 Dec '10

Since I could not contact Mr. Farnham, I contact you with the observation/question below. Cheers, Harold ______________________________________________ From: Meijer, Harold Sent: Monday 20 December 2010 16:19 To: 'GAFA(a)MBA.ac.uk' Subject: Ectocarpus siliculosus Dear Mr. Farnham, During a blast I encountered a PLC annotated by you. However, I have doubts on the genemodel. Currently, it is denoted as http://bioinformatics.psb.ugent.be/webtools/bogas/annotation/Ectsi/current/… However, I have a strong feeling that the http://bioinformatics.psb.ugent.be/webtools/bogas/annotation/Ectsi/current/… should be connected via a small region between the gene models. Maybe you could have a look again and mail me your findings on this. Yours sincerely, Harold Meijer Dr. ing. Harold J. G. Meijer Wageningen University and Research Centre Plant Sciences Group Laboratory of Phytopathology Droevendaalsesteeg 1 6708 PB Wageningen The Netherlands Tel (room): +31 317 483138 fax : +31 317 483412 Email: Harold.meijer(a)wur.nl

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[Beg-bogas] account
by ACE 16 Dec '10

16 Dec '10

Dear: I need an account. Thanks. best wishes!

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[Beg-bogas] EBI HELP: INTERPROSCAN - New SOAP/REST Web Service
by User Support 10 Dec '10

10 Dec '10

Hi folks, A new InterProScan service is now available providing REST and document/literal SOAP interfaces. These have been tested extensively and are now ready for production. The present versions of this interface are scheduled for retirement mid February 2011. Please provide feedback on any issues encountered and any suggestions for additional features using http://www.ebi.ac.uk/support/. For details see the documentation: InterProScan (REST) http://www.ebi.ac.uk/Tools/webservices/services/pfa/iprscan_rest InterProScan (SOAP) http://www.ebi.ac.uk/Tools/webservices/services/pfa/iprscan_soap All the best, Support@Ebi

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[Beg-bogas] EBI HELP: INTERPROSCAN - New SOAP/REST Web Service
by User Support 10 Dec '10

10 Dec '10

Hi folks, A new InterProScan service is now available providing REST and document/literal SOAP interfaces. These have been tested extensively and are now ready for production. The present versions of this interface are scheduled for retirement mid February 2011. Please provide feedback on any issues encountered and any suggestions for additional features using http://www.ebi.ac.uk/support/. For details see the documentation: InterProScan (REST) http://www.ebi.ac.uk/Tools/webservices/services/pfa/iprscan_rest InterProScan (SOAP) http://www.ebi.ac.uk/Tools/webservices/services/pfa/iprscan_soap All the best, Support@Ebi

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[Beg-bogas] novice annotator has problem
by David Nelson 05 Dec '10

05 Dec '10

Dear help, I have annotated the pseudogene Solyc04g079620.1.1 I merged it with its two neighbors (one on each side). I saved it and it looks the way I intended in ANNOJ and Genome View, but the BOGAS page is empty. Can you tell me why? What did I do wrong? When I saved the three merged models in Genome View I chose to delete the obsolete structures. Did this eliminate the BOGAS models? -- David R. Nelson Associate Professor Dept. of Microbiology, Immunology and Biochemistry 858 Madison Ave. Suite G01 University of Tennessee Memphis TN 38163 (901) 448-8303 phone (901) 448-7360 fax dnelson(a)uthsc.edu

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